synapse/UPGRADE.rst

Upgrading to v1.20.0

Shared rooms endpoint (MSC2666)

This release contains a new unstable endpoint /_matrix/client/unstable/uk.half-shot.msc2666/user/shared_rooms/.* for fetching rooms one user has in common with another. This feature requires the update_user_directory config flag to be True. If you are you are using a synapse.app.user_dir worker, requests to this endpoint must be handled by that worker. See docs/workers.md for more details.

Upgrading Synapse

Before upgrading check if any special steps are required to upgrade from the version you currently have installed to the current version of Synapse. The extra instructions that may be required are listed later in this document.

• If Synapse was installed using prebuilt packages, you will need to follow the normal process for upgrading those packages.
• If Synapse was installed from source, then:

  1. Activate the virtualenv before upgrading. For example, if Synapse is installed in a virtualenv in ~/synapse/env then run:

     source ~/synapse/env/bin/activate

  2. If Synapse was installed using pip then upgrade to the latest version by running:

     pip install --upgrade matrix-synapse

     If Synapse was installed using git then upgrade to the latest version by running:

     git pull
     pip install --upgrade .

  3. Restart Synapse:

     ./synctl restart

To check whether your update was successful, you can check the running server version with:

# you may need to replace 'localhost:8008' if synapse is not configured
# to listen on port 8008.

curl http://localhost:8008/_synapse/admin/v1/server_version

Rolling back to older versions

Rolling back to previous releases can be difficult, due to database schema changes between releases. Where we have been able to test the rollback process, this will be noted below.

In general, you will need to undo any changes made during the upgrade process, for example:

• pip:

  source env/bin/activate
  # replace `1.3.0` accordingly:
  pip install matrix-synapse==1.3.0

• Debian:

  # replace `1.3.0` and `stretch` accordingly:
  wget https://packages.matrix.org/debian/pool/main/m/matrix-synapse-py3/matrix-synapse-py3_1.3.0+stretch1_amd64.deb
  dpkg -i matrix-synapse-py3_1.3.0+stretch1_amd64.deb

Upgrading to v1.18.0

Docker -py3 suffix will be removed in future versions

From 10th August 2020, we will no longer publish Docker images with the -py3 tag suffix. The images tagged with the -py3 suffix have been identical to the non-suffixed tags since release 0.99.0, and the suffix is obsolete.

On 10th August, we will remove the latest-py3 tag. Existing per-release tags (such as v1.18.0-py3) will not be removed, but no new -py3 tags will be added.

Scripts relying on the -py3 suffix will need to be updated.

Redis replication is now recommended in lieu of TCP replication

When setting up worker processes, we now recommend the use of a Redis server for replication. The old direct TCP connection method is deprecated and will be removed in a future release. See docs/workers.md for more details.

Upgrading to v1.14.0

This version includes a database update which is run as part of the upgrade, and which may take a couple of minutes in the case of a large server. Synapse will not respond to HTTP requests while this update is taking place.

Upgrading to v1.13.0

Incorrect database migration in old synapse versions

A bug was introduced in Synapse 1.4.0 which could cause the room directory to be incomplete or empty if Synapse was upgraded directly from v1.2.1 or earlier, to versions between v1.4.0 and v1.12.x.

This will not be a problem for Synapse installations which were:

• created at v1.4.0 or later,
• upgraded via v1.3.x, or
• upgraded straight from v1.2.1 or earlier to v1.13.0 or later.

If completeness of the room directory is a concern, installations which are affected can be repaired as follows:

1. Run the following sql from a psql or sqlite3 console:

   INSERT INTO background_updates (update_name, progress_json, depends_on) VALUES
      ('populate_stats_process_rooms', '{}', 'current_state_events_membership');
   
   INSERT INTO background_updates (update_name, progress_json, depends_on) VALUES
      ('populate_stats_process_users', '{}', 'populate_stats_process_rooms');

2. Restart synapse.

New Single Sign-on HTML Templates

New templates (sso_auth_confirm.html, sso_auth_success.html, and sso_account_deactivated.html) were added to Synapse. If your Synapse is configured to use SSO and a custom sso_redirect_confirm_template_dir configuration then these templates will need to be copied from synapse/res/templates into that directory.

Synapse SSO Plugins Method Deprecation

Plugins using the complete_sso_login method of synapse.module_api.ModuleApi should update to using the async/await version complete_sso_login_async which includes additional checks. The non-async version is considered deprecated.

Rolling back to v1.12.4 after a failed upgrade

v1.13.0 includes a lot of large changes. If something problematic occurs, you may want to roll-back to a previous version of Synapse. Because v1.13.0 also includes a new database schema version, reverting that version is also required alongside the generic rollback instructions mentioned above. In short, to roll back to v1.12.4 you need to:

1. Stop the server

2. Decrease the schema version in the database:

   UPDATE schema_version SET version = 57;

3. Downgrade Synapse by following the instructions for your installation method in the "Rolling back to older versions" section above.

Upgrading to v1.12.0

This version includes a database update which is run as part of the upgrade, and which may take some time (several hours in the case of a large server). Synapse will not respond to HTTP requests while this update is taking place.

This is only likely to be a problem in the case of a server which is participating in many rooms.

0. As with all upgrades, it is recommended that you have a recent backup of your database which can be used for recovery in the event of any problems.

1. As an initial check to see if you will be affected, you can try running the following query from the psql or sqlite3 console. It is safe to run it while Synapse is still running.

   SELECT MAX(q.v) FROM (
     SELECT (
       SELECT ej.json AS v
       FROM state_events se INNER JOIN event_json ej USING (event_id)
       WHERE se.room_id=rooms.room_id AND se.type='m.room.create' AND se.state_key=''
       LIMIT 1
     ) FROM rooms WHERE rooms.room_version IS NULL
   ) q;

   This query will take about the same amount of time as the upgrade process: ie, if it takes 5 minutes, then it is likely that Synapse will be unresponsive for 5 minutes during the upgrade.

   If you consider an outage of this duration to be acceptable, no further action is necessary and you can simply start Synapse 1.12.0.

   If you would prefer to reduce the downtime, continue with the steps below.

2. The easiest workaround for this issue is to manually create a new index before upgrading. On PostgreSQL, his can be done as follows:

   CREATE INDEX CONCURRENTLY tmp_upgrade_1_12_0_index
   ON state_events(room_id) WHERE type = 'm.room.create';

   The above query may take some time, but is also safe to run while Synapse is running.

   We assume that no SQLite users have databases large enough to be affected. If you are affected, you can run a similar query, omitting the CONCURRENTLY keyword. Note however that this operation may in itself cause Synapse to stop running for some time. Synapse admins are reminded that SQLite is not recommended for use outside a test environment.

3. Once the index has been created, the SELECT query in step 1 above should complete quickly. It is therefore safe to upgrade to Synapse 1.12.0.

4. Once Synapse 1.12.0 has successfully started and is responding to HTTP requests, the temporary index can be removed:

   DROP INDEX tmp_upgrade_1_12_0_index;

Upgrading to v1.10.0

Synapse will now log a warning on start up if used with a PostgreSQL database that has a non-recommended locale set.

See docs/postgres.md for details.

Upgrading to v1.8.0

Specifying a log_file config option will now cause Synapse to refuse to start, and should be replaced by with the log_config option. Support for the log_file option was removed in v1.3.0 and has since had no effect.

Upgrading to v1.7.0

In an attempt to configure Synapse in a privacy preserving way, the default behaviours of allow_public_rooms_without_auth and allow_public_rooms_over_federation have been inverted. This means that by default, only authenticated users querying the Client/Server API will be able to query the room directory, and relatedly that the server will not share room directory information with other servers over federation.

If your installation does not explicitly set these settings one way or the other and you want either setting to be true then it will necessary to update your homeserver configuration file accordingly.

For more details on the surrounding context see our explainer.

Upgrading to v1.5.0

This release includes a database migration which may take several minutes to complete if there are a large number (more than a million or so) of entries in the devices table. This is only likely to a be a problem on very large installations.

Upgrading to v1.4.0

New custom templates

If you have configured a custom template directory with the email.template_dir option, be aware that there are new templates regarding registration and threepid management (see below) that must be included.

• registration.html and registration.txt
• registration_success.html and registration_failure.html
• add_threepid.html and add_threepid.txt
• add_threepid_failure.html and add_threepid_success.html

Synapse will expect these files to exist inside the configured template directory, and will fail to start if they are absent. To view the default templates, see synapse/res/templates.

3pid verification changes

Note: As of this release, users will be unable to add phone numbers or email addresses to their accounts, without changes to the Synapse configuration. This includes adding an email address during registration.

It is possible for a user to associate an email address or phone number with their account, for a number of reasons:

• for use when logging in, as an alternative to the user id.
• in the case of email, as an alternative contact to help with account recovery.
• in the case of email, to receive notifications of missed messages.

Before an email address or phone number can be added to a user's account, or before such an address is used to carry out a password-reset, Synapse must confirm the operation with the owner of the email address or phone number. It does this by sending an email or text giving the user a link or token to confirm receipt. This process is known as '3pid verification'. ('3pid', or 'threepid', stands for third-party identifier, and we use it to refer to external identifiers such as email addresses and phone numbers.)

Previous versions of Synapse delegated the task of 3pid verification to an identity server by default. In most cases this server is vector.im or matrix.org.

In Synapse 1.4.0, for security and privacy reasons, the homeserver will no longer delegate this task to an identity server by default. Instead, the server administrator will need to explicitly decide how they would like the verification messages to be sent.

In the medium term, the vector.im and matrix.org identity servers will disable support for delegated 3pid verification entirely. However, in order to ease the transition, they will retain the capability for a limited period. Delegated email verification will be disabled on Monday 2nd December 2019 (giving roughly 2 months notice). Disabling delegated SMS verification will follow some time after that once SMS verification support lands in Synapse.

Once delegated 3pid verification support has been disabled in the vector.im and matrix.org identity servers, all Synapse versions that depend on those instances will be unable to verify email and phone numbers through them. There are no imminent plans to remove delegated 3pid verification from Sydent generally. (Sydent is the identity server project that backs the vector.im and matrix.org instances).

Email

Following upgrade, to continue verifying email (e.g. as part of the registration process), admins can either:-

• Configure Synapse to use an email server.
• Run or choose an identity server which allows delegated email verification and delegate to it.

Configure SMTP in Synapse

To configure an SMTP server for Synapse, modify the configuration section headed email, and be sure to have at least the smtp_host, smtp_port and notif_from fields filled out.

You may also need to set smtp_user, smtp_pass, and require_transport_security.

See the sample configuration file for more details on these settings.

Delegate email to an identity server

Some admins will wish to continue using email verification as part of the registration process, but will not immediately have an appropriate SMTP server at hand.

To this end, we will continue to support email verification delegation via the vector.im and matrix.org identity servers for two months. Support for delegated email verification will be disabled on Monday 2nd December.

The account_threepid_delegates dictionary defines whether the homeserver should delegate an external server (typically an identity server) to handle sending confirmation messages via email and SMS.

So to delegate email verification, in homeserver.yaml, set account_threepid_delegates.email to the base URL of an identity server. For example:

account_threepid_delegates:
    email: https://example.com     # Delegate email sending to example.com

Note that account_threepid_delegates.email replaces the deprecated email.trust_identity_server_for_password_resets: if email.trust_identity_server_for_password_resets is set to true, and account_threepid_delegates.email is not set, then the first entry in trusted_third_party_id_servers will be used as the account_threepid_delegate for email. This is to ensure compatibility with existing Synapse installs that set up external server handling for these tasks before v1.4.0. If email.trust_identity_server_for_password_resets is true and no trusted identity server domains are configured, Synapse will report an error and refuse to start.

If email.trust_identity_server_for_password_resets is false or absent and no email delegate is configured in account_threepid_delegates, then Synapse will send email verification messages itself, using the configured SMTP server (see above). that type.

Phone numbers

Synapse does not support phone-number verification itself, so the only way to maintain the ability for users to add phone numbers to their accounts will be by continuing to delegate phone number verification to the matrix.org and vector.im identity servers (or another identity server that supports SMS sending).

The account_threepid_delegates dictionary defines whether the homeserver should delegate an external server (typically an identity server) to handle sending confirmation messages via email and SMS.

So to delegate phone number verification, in homeserver.yaml, set account_threepid_delegates.msisdn to the base URL of an identity server. For example:

account_threepid_delegates:
    msisdn: https://example.com     # Delegate sms sending to example.com

The matrix.org and vector.im identity servers will continue to support delegated phone number verification via SMS until such time as it is possible for admins to configure their servers to perform phone number verification directly. More details will follow in a future release.

Rolling back to v1.3.1

If you encounter problems with v1.4.0, it should be possible to roll back to v1.3.1, subject to the following:

• The 'room statistics' engine was heavily reworked in this release (see #5971), including significant changes to the database schema, which are not easily reverted. This will cause the room statistics engine to stop updating when you downgrade.

  The room statistics are essentially unused in v1.3.1 (in future versions of Synapse, they will be used to populate the room directory), so there should be no loss of functionality. However, the statistics engine will write errors to the logs, which can be avoided by setting the following in `homeserver.yaml`:

  stats:
    enabled: false

  Don't forget to re-enable it when you upgrade again, in preparation for its use in the room directory!

Upgrading to v1.2.0

Some counter metrics have been renamed, with the old names deprecated. See the metrics documentation for details.

Upgrading to v1.1.0

Synapse v1.1.0 removes support for older Python and PostgreSQL versions, as outlined in our deprecation notice.

Minimum Python Version

Synapse v1.1.0 has a minimum Python requirement of Python 3.5. Python 3.6 or Python 3.7 are recommended as they have improved internal string handling, significantly reducing memory usage.

If you use current versions of the Matrix.org-distributed Debian packages or Docker images, action is not required.

If you install Synapse in a Python virtual environment, please see "Upgrading to v0.34.0" for notes on setting up a new virtualenv under Python 3.

Minimum PostgreSQL Version

If using PostgreSQL under Synapse, you will need to use PostgreSQL 9.5 or above. Please see the PostgreSQL documentation for more details on upgrading your database.

Upgrading to v1.0

Validation of TLS certificates

Synapse v1.0 is the first release to enforce validation of TLS certificates for the federation API. It is therefore essential that your certificates are correctly configured. See the FAQ for more information.

Note, v1.0 installations will also no longer be able to federate with servers that have not correctly configured their certificates.

In rare cases, it may be desirable to disable certificate checking: for example, it might be essential to be able to federate with a given legacy server in a closed federation. This can be done in one of two ways:-

• Configure the global switch federation_verify_certificates to false.
• Configure a whitelist of server domains to trust via federation_certificate_verification_whitelist.

See the sample configuration file for more details on these settings.

Email

When a user requests a password reset, Synapse will send an email to the user to confirm the request.

Previous versions of Synapse delegated the job of sending this email to an identity server. If the identity server was somehow malicious or became compromised, it would be theoretically possible to hijack an account through this means.

Therefore, by default, Synapse v1.0 will send the confirmation email itself. If Synapse is not configured with an SMTP server, password reset via email will be disabled.

To configure an SMTP server for Synapse, modify the configuration section headed email, and be sure to have at least the smtp_host, smtp_port and notif_from fields filled out. You may also need to set smtp_user, smtp_pass, and require_transport_security.

If you are absolutely certain that you wish to continue using an identity server for password resets, set trust_identity_server_for_password_resets to true.

See the sample configuration file for more details on these settings.

New email templates ---------------Some new templates have been added to the default template directory for the purpose of the homeserver sending its own password reset emails. If you have configured a custom template_dir in your Synapse config, these files will need to be added.

password_reset.html and password_reset.txt are HTML and plain text templates respectively that contain the contents of what will be emailed to the user upon attempting to reset their password via email. password_reset_success.html and password_reset_failure.html are HTML files that the content of which (assuming no redirect URL is set) will be shown to the user after they attempt to click the link in the email sent to them.

Upgrading to v0.99.0

Please be aware that, before Synapse v1.0 is released around March 2019, you will need to replace any self-signed certificates with those verified by a root CA. Information on how to do so can be found at the ACME docs.

For more information on configuring TLS certificates see the FAQ.

Upgrading to v0.34.0

1. This release is the first to fully support Python 3. Synapse will now run on Python versions 3.5, or 3.6 (as well as 2.7). We recommend switching to Python 3, as it has been shown to give performance improvements.

   For users who have installed Synapse into a virtualenv, we recommend doing this by creating a new virtualenv. For example:

   virtualenv -p python3 ~/synapse/env3
   source ~/synapse/env3/bin/activate
   pip install matrix-synapse

   You can then start synapse as normal, having activated the new virtualenv:

   cd ~/synapse
   source env3/bin/activate
   synctl start

   Users who have installed from distribution packages should see the relevant package documentation. See below for notes on Debian packages.

   • When upgrading to Python 3, you must make sure that your log files are configured as UTF-8, by adding encoding: utf8 to the RotatingFileHandler configuration (if you have one) in your <server>.log.config file. For example, if your log.config file contains:

     handlers:
       file:
         class: logging.handlers.RotatingFileHandler
         formatter: precise
         filename: homeserver.log
         maxBytes: 104857600
         backupCount: 10
         filters: [context]
       console:
         class: logging.StreamHandler
         formatter: precise
         filters: [context]

     Then you should update this to be:

     handlers:
       file:
         class: logging.handlers.RotatingFileHandler
         formatter: precise
         filename: homeserver.log
         maxBytes: 104857600
         backupCount: 10
         filters: [context]
         encoding: utf8
       console:
         class: logging.StreamHandler
         formatter: precise
         filters: [context]

     There is no need to revert this change if downgrading to Python 2.

   We are also making available Debian packages which will run Synapse on Python 3. You can switch to these packages with apt-get install matrix-synapse-py3, however, please read debian/NEWS before doing so. The existing matrix-synapse packages will continue to use Python 2 for the time being.

2. This release removes the riot.im from the default list of trusted identity servers.

   If riot.im is in your homeserver's list of trusted_third_party_id_servers, you should remove it. It was added in case a hypothetical future identity server was put there. If you don't remove it, users may be unable to deactivate their accounts.

3. This release no longer installs the (unmaintained) Matrix Console web client as part of the default installation. It is possible to re-enable it by installing it separately and setting the web_client_location config option, but please consider switching to another client.

Upgrading to v0.33.7

This release removes the example email notification templates from res/templates (they are now internal to the python package). This should only affect you if you (a) deploy your Synapse instance from a git checkout or a github snapshot URL, and (b) have email notifications enabled.

If you have email notifications enabled, you should ensure that email.template_dir is either configured to point at a directory where you have installed customised templates, or leave it unset to use the default templates.

Upgrading to v0.27.3

This release expands the anonymous usage stats sent if the opt-in report_stats configuration is set to true. We now capture RSS memory and cpu use at a very coarse level. This requires administrators to install the optional psutil python module.

We would appreciate it if you could assist by ensuring this module is available and report_stats is enabled. This will let us see if performance changes to synapse are having an impact to the general community.

Upgrading to v0.15.0

If you want to use the new URL previewing API (/_matrix/media/r0/preview_url) then you have to explicitly enable it in the config and update your dependencies dependencies. See README.rst for details.

Upgrading to v0.11.0

This release includes the option to send anonymous usage stats to matrix.org, and requires that administrators explictly opt in or out by setting the report_stats option to either true or false.

We would really appreciate it if you could help our project out by reporting anonymized usage statistics from your homeserver. Only very basic aggregate data (e.g. number of users) will be reported, but it helps us to track the growth of the Matrix community, and helps us to make Matrix a success, as well as to convince other networks that they should peer with us.

Upgrading to v0.9.0

Application services have had a breaking API change in this version.

They can no longer register themselves with a home server using the AS HTTP API. This decision was made because a compromised application service with free reign to register any regex in effect grants full read/write access to the home server if a regex of .* is used. An attack where a compromised AS re-registers itself with .* was deemed too big of a security risk to ignore, and so the ability to register with the HS remotely has been removed.

It has been replaced by specifying a list of application service registrations in homeserver.yaml:

app_service_config_files: ["registration-01.yaml", "registration-02.yaml"]

Where registration-01.yaml looks like:

url: <String>  # e.g. "https://my.application.service.com"
as_token: <String>
hs_token: <String>
sender_localpart: <String>  # This is a new field which denotes the user_id localpart when using the AS token
namespaces:
  users:
    - exclusive: <Boolean>
      regex: <String>  # e.g. "@prefix_.*"
  aliases:
    - exclusive: <Boolean>
      regex: <String>
  rooms:
    - exclusive: <Boolean>
      regex: <String>

Upgrading to v0.8.0

Servers which use captchas will need to add their public key to:

static/client/register/register_config.js

  window.matrixRegistrationConfig = {
      recaptcha_public_key: "YOUR_PUBLIC_KEY"
  };

This is required in order to support registration fallback (typically used on mobile devices).

Upgrading to v0.7.0

New dependencies are:

• pydenticon
• simplejson
• syutil
• matrix-angular-sdk

To pull in these dependencies in a virtual env, run:

python synapse/python_dependencies.py | xargs -n 1 pip install

Upgrading to v0.6.0

To pull in new dependencies, run:

python setup.py develop --user

This update includes a change to the database schema. To upgrade you first need to upgrade the database by running:

python scripts/upgrade_db_to_v0.6.0.py <db> <server_name> <signing_key>

Where <db> is the location of the database, <server_name> is the server name as specified in the synapse configuration, and <signing_key> is the location of the signing key as specified in the synapse configuration.

This may take some time to complete. Failures of signatures and content hashes can safely be ignored.

Upgrading to v0.5.1

Depending on precisely when you installed v0.5.0 you may have ended up with a stale release of the reference matrix webclient installed as a python module. To uninstall it and ensure you are depending on the latest module, please run:

$ pip uninstall syweb

Upgrading to v0.5.0

The webclient has been split out into a seperate repository/pacakage in this release. Before you restart your homeserver you will need to pull in the webclient package by running:

python setup.py develop --user

This release completely changes the database schema and so requires upgrading it before starting the new version of the homeserver.

The script "database-prepare-for-0.5.0.sh" should be used to upgrade the database. This will save all user information, such as logins and profiles, but will otherwise purge the database. This includes messages, which rooms the home server was a member of and room alias mappings.

If you would like to keep your history, please take a copy of your database file and ask for help in #matrix:matrix.org. The upgrade process is, unfortunately, non trivial and requires human intervention to resolve any resulting conflicts during the upgrade process.

Before running the command the homeserver should be first completely shutdown. To run it, simply specify the location of the database, e.g.:

./scripts/database-prepare-for-0.5.0.sh "homeserver.db"

Once this has successfully completed it will be safe to restart the homeserver. You may notice that the homeserver takes a few seconds longer to restart than usual as it reinitializes the database.

On startup of the new version, users can either rejoin remote rooms using room aliases or by being reinvited. Alternatively, if any other homeserver sends a message to a room that the homeserver was previously in the local HS will automatically rejoin the room.

Upgrading to v0.4.0

This release needs an updated syutil version. Run:

python setup.py develop

You will also need to upgrade your configuration as the signing key format has changed. Run:

python -m synapse.app.homeserver --config-path <CONFIG> --generate-config

Upgrading to v0.3.0

This registration API now closely matches the login API. This introduces a bit more backwards and forwards between the HS and the client, but this improves the overall flexibility of the API. You can now GET on /register to retrieve a list of valid registration flows. Upon choosing one, they are submitted in the same way as login, e.g:

{
  type: m.login.password,
  user: foo,
  password: bar
}

The default HS supports 2 flows, with and without Identity Server email authentication. Enabling captcha on the HS will add in an extra step to all flows: m.login.recaptcha which must be completed before you can transition to the next stage. There is a new login type: m.login.email.identity which contains the threepidCreds key which were previously sent in the original register request. For more information on this, see the specification.

Web Client

The VoIP specification has changed between v0.2.0 and v0.3.0. Users should refresh any browser tabs to get the latest web client code. Users on v0.2.0 of the web client will not be able to call those on v0.3.0 and vice versa.

Upgrading to v0.2.0

The home server now requires setting up of SSL config before it can run. To automatically generate default config use:

$ python synapse/app/homeserver.py \
    --server-name machine.my.domain.name \
    --bind-port 8448 \
    --config-path homeserver.config \
    --generate-config

This config can be edited if desired, for example to specify a different SSL certificate to use. Once done you can run the home server using:

$ python synapse/app/homeserver.py --config-path homeserver.config

See the README.rst for more information.

Also note that some config options have been renamed, including:

• "host" to "server-name"
• "database" to "database-path"
• "port" to "bind-port" and "unsecure-port"

Upgrading to v0.0.1

This release completely changes the database schema and so requires upgrading it before starting the new version of the homeserver.

The script "database-prepare-for-0.0.1.sh" should be used to upgrade the database. This will save all user information, such as logins and profiles, but will otherwise purge the database. This includes messages, which rooms the home server was a member of and room alias mappings.

Before running the command the homeserver should be first completely shutdown. To run it, simply specify the location of the database, e.g.:

./scripts/database-prepare-for-0.0.1.sh "homeserver.db"

Once this has successfully completed it will be safe to restart the homeserver. You may notice that the homeserver takes a few seconds longer to restart than usual as it reinitializes the database.

On startup of the new version, users can either rejoin remote rooms using room aliases or by being reinvited. Alternatively, if any other homeserver sends a message to a room that the homeserver was previously in the local HS will automatically rejoin the room.